help > Setup Pipeline error: "mismatched dimensions"
Showing 1-9 of 9 posts
Apr 5, 2017 12:04 PM | Sascha Froelich
Setup Pipeline error: "mismatched dimensions"
Hello,
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
This is my preprocessing pipeline (in order):
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
ERROR: Subject XXX Session 1 first-level
covariate realignment mismatched dimensions (250 rows, while
functional data has 245 scans; the number of rows of a first-level
covariate should equal the number of scans for this
subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
This is my preprocessing pipeline (in order):
-functional Slice-time correction
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
Apr 5, 2017 09:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Setup Pipeline error: "mismatched dimensions"
Hi Sascha
Simply placing the "functional removal of initial scans" step at the beginning of your pipeline (instead of at the end) should work without a problem. The error that you describe is arising because your first-level covariates are being created during the "realignment" and the "outlier detection" steps (before the initial five scans are being removed) so they end up having different lengths / number of timepoints than your functional data (which is not cropped until later in that pipeline). Moving the "functional removal" step before realignment will fix this issue (and yes, I will see if I can make CONN a bit smarter and have it crop the first-level covariates automatically when using the "functional removal of initial scans" step in order to avoid this issue in the future, thanks for pointing this issue out)
Hope this helps
Alfonso
Originally posted by Sascha Froelich:
Simply placing the "functional removal of initial scans" step at the beginning of your pipeline (instead of at the end) should work without a problem. The error that you describe is arising because your first-level covariates are being created during the "realignment" and the "outlier detection" steps (before the initial five scans are being removed) so they end up having different lengths / number of timepoints than your functional data (which is not cropped until later in that pipeline). Moving the "functional removal" step before realignment will fix this issue (and yes, I will see if I can make CONN a bit smarter and have it crop the first-level covariates automatically when using the "functional removal of initial scans" step in order to avoid this issue in the future, thanks for pointing this issue out)
Hope this helps
Alfonso
Originally posted by Sascha Froelich:
Hello,
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
This is my preprocessing pipeline (in order):
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
ERROR: Subject XXX Session 1 first-level
covariate realignment mismatched dimensions (250 rows, while
functional data has 245 scans; the number of rows of a first-level
covariate should equal the number of scans for this
subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
This is my preprocessing pipeline (in order):
-functional Slice-time correction
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
Apr 11, 2017 08:04 AM | Sascha Froelich
RE: Setup Pipeline error: "mismatched dimensions"
Dear Alfonso,
thank you for your helpful reply! I now put "functional removal of initial scans" at the top and it worked just fine.
Best,
Sascha
thank you for your helpful reply! I now put "functional removal of initial scans" at the top and it worked just fine.
Best,
Sascha
Apr 28, 2017 09:04 AM | Matti Gärtner
RE: Setup Pipeline error: "mismatched dimensions"
Hi,
probably just a minor thing, but for me the combination 'functional_removescans' doesn't work in combination with 'default_mni'
%batch.Setup.preprocessing.steps={'functional_removescans' 'default_mni'};
unknown step: 'default_mni'
I think its because of the code that prevents 'default_mni' being "unpacked" if used with other steps. Is there a specific reason for this?
conn_setup_preproc: if ~isempty(STEPS)&&(ischar(STEPS)||(iscell(STEPS)&&numel(STEPS)==1))
Best wishes,
Matti
probably just a minor thing, but for me the combination 'functional_removescans' doesn't work in combination with 'default_mni'
%batch.Setup.preprocessing.steps={'functional_removescans' 'default_mni'};
unknown step: 'default_mni'
I think its because of the code that prevents 'default_mni' being "unpacked" if used with other steps. Is there a specific reason for this?
conn_setup_preproc: if ~isempty(STEPS)&&(ischar(STEPS)||(iscell(STEPS)&&numel(STEPS)==1))
Best wishes,
Matti
Jul 28, 2022 10:07 PM | Raoul Hernandez
RE: Setup Pipeline error: "mismatched dimensions"
Cheers Alfonso,
New to CONN and love it so far (including this helpful forum - very nice!).
I feel like I am having a similar issue with my analysis. Here is the error I get when I select Done. Interestingly, I have no QC_timeseries or scrubbing files after preprocessing.
ERROR: Subject 1 Session 1 first-level covariate QC_timeseries mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 1 first-level covariate scrubbing mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
Would you suggest the same resolution for my issue?
Cheers,
Raoul
New to CONN and love it so far (including this helpful forum - very nice!).
I feel like I am having a similar issue with my analysis. Here is the error I get when I select Done. Interestingly, I have no QC_timeseries or scrubbing files after preprocessing.
ERROR: Subject 1 Session 1 first-level covariate QC_timeseries mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 1 first-level covariate scrubbing mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
Would you suggest the same resolution for my issue?
Cheers,
Raoul
Aug 1, 2022 08:08 PM | Alfonso Nieto-Castanon - Boston University
RE: Setup Pipeline error: "mismatched dimensions"
Hi Raoul,
Well, in your case I believe the issue may be simply some empty QC_timeseries 1st-level covariate files. Typically those QC_timeseries covariates are filled automatically by the preprocessing steps during the ART (outlier detection) step. Have your data been preprocessed in CONN? If so please check if you got any error message during preprocessing which may explain why the ART step did not get to run/finish correctly
Best
Alfonso
Originally posted by Raoul Hernandez:
Well, in your case I believe the issue may be simply some empty QC_timeseries 1st-level covariate files. Typically those QC_timeseries covariates are filled automatically by the preprocessing steps during the ART (outlier detection) step. Have your data been preprocessed in CONN? If so please check if you got any error message during preprocessing which may explain why the ART step did not get to run/finish correctly
Best
Alfonso
Originally posted by Raoul Hernandez:
Cheers Alfonso,
New to CONN and love it so far (including this helpful forum - very nice!).
I feel like I am having a similar issue with my analysis. Here is the error I get when I select Done. Interestingly, I have no QC_timeseries or scrubbing files after preprocessing.
ERROR: Subject 1 Session 1 first-level covariate QC_timeseries mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 1 first-level covariate scrubbing mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
Would you suggest the same resolution for my issue?
Cheers,
Raoul
New to CONN and love it so far (including this helpful forum - very nice!).
I feel like I am having a similar issue with my analysis. Here is the error I get when I select Done. Interestingly, I have no QC_timeseries or scrubbing files after preprocessing.
ERROR: Subject 1 Session 1 first-level covariate QC_timeseries mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 1 first-level covariate scrubbing mismatched dimensions (0 rows, while functional data has 200 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
Would you suggest the same resolution for my issue?
Cheers,
Raoul
Aug 3, 2022 02:08 PM | Raoul Hernandez
RE: Setup Pipeline error: "mismatched dimensions
Alfonso,
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Aug 20, 2022 02:08 PM | Raoul Hernandez
RE: Setup Pipeline error: "mismatched dimensions
Hello,
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Alfonso,
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Aug 29, 2022 06:08 PM | Alfonso Nieto-Castanon - Boston University
RE: Setup Pipeline error: "mismatched dimensions
Hi Raoul,
Not sure, this is a bit strange, the error was reporting that your functional data had 200 scans, but from the logs it seems it had 192 scans, so perhaps those logs may not correspond to the latest preprocessing of your data?. There is also the perhaps-related issue of preprocessing your data multiple times: from the file names (e.g. swauswau5001_resting.nii) it appears that your data had been already fully preprocessed at least twice ('s' indicates smoothing, 'w' normalization, 'a' slice-timing correction, and 'u' realignment, and these letters get prepended to your file names each time you run one of those steps). I would probably recommend reimporting your original data into CONN, and running preprocessing just once (e.g. if the original input filenames are "5001_resting.nii" the fully preprocessed data will be named just "swau5001_resting.nii") and seeing whether that seems to fix this issue
Hope this helps
Alfonso
Originally posted by Raoul Hernandez:
Not sure, this is a bit strange, the error was reporting that your functional data had 200 scans, but from the logs it seems it had 192 scans, so perhaps those logs may not correspond to the latest preprocessing of your data?. There is also the perhaps-related issue of preprocessing your data multiple times: from the file names (e.g. swauswau5001_resting.nii) it appears that your data had been already fully preprocessed at least twice ('s' indicates smoothing, 'w' normalization, 'a' slice-timing correction, and 'u' realignment, and these letters get prepended to your file names each time you run one of those steps). I would probably recommend reimporting your original data into CONN, and running preprocessing just once (e.g. if the original input filenames are "5001_resting.nii" the fully preprocessed data will be named just "swau5001_resting.nii") and seeing whether that seems to fix this issue
Hope this helps
Alfonso
Originally posted by Raoul Hernandez:
Hello,
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Alfonso,
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul